2GSY

The 2.6A structure of Infectious Bursal Virus Derived T=1 Particles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.6-angstrom structure of infectious bursal disease virus-derived t=1 particles reveals new stabilizing elements of the virus capsid.

Garriga, D.Querol-Audi, J.Abaitua, F.Saugar, I.Pous, J.Verdaguer, N.Caston, J.R.Rodriguez, J.F.

(2006) J.Virol. 80: 6895-6905

  • DOI: 10.1128/JVI.00368-06

  • PubMed Abstract: 
  • Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is a double-stranded RNA virus that causes a highly contagious disease in young chickens leading to significant economic losses in the poultry industry. The VP2 protein, the ...

    Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is a double-stranded RNA virus that causes a highly contagious disease in young chickens leading to significant economic losses in the poultry industry. The VP2 protein, the only structural component of the IBDV icosahedral capsid, spontaneously assembles into T=1 subviral particles (SVP) when individually expressed as a chimeric gene. We have determined the crystal structure of the T=1 SVP to 2.60 A resolution. Our results show that the 20 trimeric VP2 clusters forming the T=1 shell are further stabilized by calcium ions located at the threefold icosahedral axes. The structure also reveals a new unexpected domain swapping that mediates interactions between adjacent trimers: a short helical segment located close to the end of the long C-terminal arm of VP2 is projected toward the threefold axis of a neighboring VP2 trimer, leading to a complex network of interactions that increases the stability of the T=1 particles. Analysis of crystal packing shows that the exposed capsid residues, His253 and Thr284, determinants of IBDV virulence and the adaptation of the virus to grow in cell culture, are involved in particle-particle interactions.


    Organizational Affiliation

    Institut de Biologia Molecular Barcelona, CSIC, Josep Samitier 1-5, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
polyprotein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
456Avian infectious bursal disease virusMutation(s): 0 
Find proteins for P61825 (Avian infectious bursal disease virus)
Go to UniProtKB:  P61825
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, F, G, L, M, O, S, T
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.254 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 326.300α = 90.00
b = 326.300β = 90.00
c = 326.300γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance